Connect it to one of the ADC pins which also connects to a comparator (pins 9, 12, 15 and 18 on the 48-pin device). Use the comparator output to trigger the A/D.
That leaves one question unanswered - where to connect the other comparator input.
If you know the voltage of the low part of the waveform, connect it to a suitable point on the voltage divider, if you don't, connect a resistor one end to your signal, and the other end to the comparator input, then connect a capacitor from the comparator input to 0V. Resistor and capacitor values will depend on the frequency (which you didn't state).
Alternatively, (and this depends on the frequency and mark-space ratio of your signal). Sample at a frequency that makes sure you get at least one sample in the high part of the waveform. Then filter the output with a simple IIR filter. Compare the latest sample with the output of the filter. If the sample is higher than the filter that is your "high" voltage.
A simple IIR filter: (latest sample in R0, running total in R1, output in R2, n is the time constant)
SUBS R1,R1,R1,LSR#n
ADDS R1,R1,R0
LSRS R2,R1,#n
or, combining it with the comparator so it now only needs two registers:
SUBS R1,R1,R1,LSR #n
ADDS R1,R1,R0
CMP R0,R1,LSR #n